CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer Class Reference

Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph. More...

#include <MMFF94VanDerWaalsInteractionParameterizer.hpp>

Public Types
typedef std::shared_ptr< MMFF94VanDerWaalsInteractionParameterizer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94VanDerWaalsInteractionParameterizer instances. More...

Public Member Functions
	MMFF94VanDerWaalsInteractionParameterizer ()
	Constructs an MMFF94VanDerWaalsInteractionParameterizer instance using the default MMFF94 parameter tables. More...
	MMFF94VanDerWaalsInteractionParameterizer (const Chem::MolecularGraph &molgraph, MMFF94VanDerWaalsInteractionList &ia_list, bool strict)
	Constructs the parameterizer and processes the molecular graph molgraph. More...
void	setFilterFunction (const InteractionFilterFunction2 &func)
	Sets the filter function used to skip atom pairs during parameterization. More...
void	setAtomTypeFunction (const MMFF94NumericAtomTypeFunction &func)
	Sets the function used to look up the MMFF94 numeric atom type of an atom. More...
void	setTopologicalDistanceFunction (const TopologicalAtomDistanceFunction &func)
	Sets the function used to determine the topological distance between two atoms (number of bonds along the shortest path). More...
void	setVanDerWaalsParameterTable (const MMFF94VanDerWaalsParameterTable::SharedPointer &table)
	Sets the table providing MMFF94 numeric atom type Van der Waals parameters and donor/acceptor classifications. More...
void	parameterize (const Chem::MolecularGraph &molgraph, MMFF94VanDerWaalsInteractionList &ia_list, bool strict)
	Perceives the MMFF94 Van der Waals interactions for molgraph and outputs the corresponding parameter data into ia_list. More...

Detailed Description

Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph.

For every pair of atoms separated by at least three bonds the parameterizer looks up the per-atom type Van der Waals parameters and the donor/acceptor classification from the supplied parameter table, applies the MMFF94 combining rules and emits an MMFF94VanDerWaalsInteraction instance.

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<MMFF94VanDerWaalsInteractionParameterizer> CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94VanDerWaalsInteractionParameterizer instances.

Constructor & Destructor Documentation

MMFF94VanDerWaalsInteractionParameterizer() [1/2]

CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::MMFF94VanDerWaalsInteractionParameterizer

(

)

Constructs an MMFF94VanDerWaalsInteractionParameterizer instance using the default MMFF94 parameter tables.

MMFF94VanDerWaalsInteractionParameterizer() [2/2]

CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::MMFF94VanDerWaalsInteractionParameterizer	(	const Chem::MolecularGraph &	molgraph,
		MMFF94VanDerWaalsInteractionList &	ia_list,
		bool	strict
	)

Constructs the parameterizer and processes the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to parameterize the Van der Waals interactions.
ia_list	Output list receiving the generated MMFF94VanDerWaalsInteraction instances.
strict	If true, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

Member Function Documentation

setFilterFunction()

void CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::setFilterFunction

(

const InteractionFilterFunction2 &

func

)

Sets the filter function used to skip atom pairs during parameterization.

Parameters

func	The new filter function (when it returns false for an atom pair, the pair is skipped).

setAtomTypeFunction()

void CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::setAtomTypeFunction

(

const MMFF94NumericAtomTypeFunction &

func

)

Sets the function used to look up the MMFF94 numeric atom type of an atom.

Parameters

func	The new numeric atom type lookup function.

setTopologicalDistanceFunction()

void CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::setTopologicalDistanceFunction

(

const TopologicalAtomDistanceFunction &

func

)

Sets the function used to determine the topological distance between two atoms (number of bonds along the shortest path).

Parameters

func	The new topological distance function.

setVanDerWaalsParameterTable()

void CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::setVanDerWaalsParameterTable

(

const MMFF94VanDerWaalsParameterTable::SharedPointer &

table

)

Sets the table providing MMFF94 numeric atom type Van der Waals parameters and donor/acceptor classifications.

Parameters

table

The new Van der Waals parameter table.

parameterize()

void CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer::parameterize	(	const Chem::MolecularGraph &	molgraph,
		MMFF94VanDerWaalsInteractionList &	ia_list,
		bool	strict
	)

Perceives the MMFF94 Van der Waals interactions for molgraph and outputs the corresponding parameter data into ia_list.

Parameters

molgraph	The molecular graph for which to parameterize the Van der Waals interactions.
ia_list	Output list receiving the generated MMFF94VanDerWaalsInteraction instances.
strict	If true, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

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The documentation for this class was generated from the following file:

• MMFF94VanDerWaalsInteractionParameterizer.hpp